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<title>TSSr Vignette</title>

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<h1 class="title toc-ignore">TSSr Vignette</h1>
<h4 class="author">Zhaolian Lu, Keenan Berry, Zhenbin Hu, Yu Zhan, Tae-Hyuk Ahn, Zhenguo Lin</h4>
<h4 class="date">2021-10-07</h4>



<p>Alternatively, you can install the development version directly from GitHub using <code>devtools</code>:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">&quot;Linlab-slu/TSSr&quot;</span>)</span></code></pre></div>
<p>And load <code>TSSr</code>:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(TSSr)</span></code></pre></div>
<div id="citation" class="section level1">
<h1>Citation</h1>
<p>If you use TSSr, please cite the following article:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">citation</span>(<span class="st">&quot;TSSr&quot;</span>)</span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; To cite package &#39;TSSr&#39; in publications use:</span></span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   Zhaolian Lu, Keenan Berry, Zhenbin Hu, Yu Zhan, Tae-Hyuk (Ted) Ahn</span></span>
<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   and Zhenguo Lu (2021) TSS sequencing data analysis. R package version</span></span>
<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   0.99.0. URL https://github.com/Linlab-slu/TSSr</span></span>
<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; A BibTeX entry for LaTeX users is</span></span>
<span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb3-11"><a href="#cb3-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   @Manual{,</span></span>
<span id="cb3-12"><a href="#cb3-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     title = {{TSSr}: TSS sequencing data analysis},</span></span>
<span id="cb3-13"><a href="#cb3-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     author = {Zhaolian Lu and Keenan Berry and Zhenbin Hu and Yu Zhan and Tae-Hyuk Ahn and Zhenguo Lin},</span></span>
<span id="cb3-14"><a href="#cb3-14" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     year = {2021},</span></span>
<span id="cb3-15"><a href="#cb3-15" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     version = {0.99.0},</span></span>
<span id="cb3-16"><a href="#cb3-16" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     url = {https://github.com/Linlab-slu/TSSr},</span></span>
<span id="cb3-17"><a href="#cb3-17" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   }</span></span></code></pre></div>
</div>
<div id="getting-help" class="section level1">
<h1>Getting help</h1>
<p>For general questions about the usage of TSSr, use the <a href="https://support.bioconductor.org">official Bioconductor support forum</a> and tag your question “TSSr”. We strive to answer questions as quickly as possible.</p>
<p>For technical questions, bug reports and suggestions for new features, we refer to the <a href="https://github.com/Linlab-slu/TSSr/issues">TSSr github page</a>.</p>
</div>
<div id="quick-start" class="section level1">
<h1>Quick start</h1>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Load the example data</span></span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="fu">data</span>(<span class="st">&quot;exampleTSSr&quot;</span>)</span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>myTSSr <span class="ot">&lt;-</span> exampleTSSr</span></code></pre></div>
<p>Or create a new TSSr object</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Provide bam files</span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>inputFiles <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="st">&quot;S01.sorted.bam&quot;</span>, <span class="st">&quot;S02.sorted.bam&quot;</span>, <span class="st">&quot;S03.sorted.bam&quot;</span>, <span class="st">&quot;S04.sorted.bam&quot;</span>)</span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>myTSSr <span class="ot">&lt;-</span> <span class="fu">new</span>(<span class="st">&quot;TSSr&quot;</span>, <span class="at">genomeName =</span> <span class="st">&quot;BSgenome.Scerevisiae.UCSC.sacCer3&quot;</span></span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>          ,<span class="at">inputFiles =</span> inputFiles</span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>          ,<span class="at">inputFilesType=</span> <span class="st">&quot;bam&quot;</span></span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a>          ,<span class="at">sampleLabels =</span> <span class="fu">c</span>(<span class="st">&quot;SL01&quot;</span>,<span class="st">&quot;SL02&quot;</span>,<span class="st">&quot;SL03&quot;</span>,<span class="st">&quot;SL04&quot;</span>)</span>
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a>          ,<span class="at">sampleLabelsMerged =</span> <span class="fu">c</span>(<span class="st">&quot;control&quot;</span>,<span class="st">&quot;treat&quot;</span>)</span>
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a>          ,<span class="at">mergeIndex =</span> <span class="fu">c</span>(<span class="dv">1</span>,<span class="dv">1</span>,<span class="dv">2</span>,<span class="dv">2</span>)</span>
<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a>          ,<span class="at">refSource =</span> <span class="st">&quot;saccharomyces_cerevisiae.SGD.gff&quot;</span></span>
<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a>          ,<span class="at">organismName =</span> <span class="st">&quot;saccharomyces cerevisiae&quot;</span>)</span>
<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a>myTSSr</span></code></pre></div>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Get TSS</span></span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a><span class="fu">getTSS</span>(myTSSr)</span></code></pre></div>
<p>TSS data processing</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Merge replicates</span></span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="fu">mergeSamples</span>(myTSSr)</span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a><span class="co"># Normalization</span></span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a><span class="fu">normalizeTSS</span>(myTSSr)</span>
<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Normalizing TSS matrix...</span></span>
<span id="cb7-7"><a href="#cb7-7" aria-hidden="true" tabindex="-1"></a><span class="co"># TSS filtering</span></span>
<span id="cb7-8"><a href="#cb7-8" aria-hidden="true" tabindex="-1"></a><span class="fu">filterTSS</span>(myTSSr, <span class="at">method =</span> <span class="st">&quot;TPM&quot;</span>, <span class="at">tpmLow =</span> <span class="fl">0.1</span>)</span>
<span id="cb7-9"><a href="#cb7-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb7-10"><a href="#cb7-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Filtering data with TPM method...</span></span></code></pre></div>
<p>TSS clustering</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="co"># TSS clustering </span></span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="fu">clusterTSS</span>(myTSSr, <span class="at">method =</span> <span class="st">&quot;peakclu&quot;</span>,<span class="at">peakDistance=</span><span class="dv">100</span>,<span class="at">extensionDistance=</span><span class="dv">30</span></span>
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>         ,<span class="at">localThreshold =</span> <span class="fl">0.02</span>,<span class="at">clusterThreshold =</span> <span class="dv">1</span></span>
<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a>         ,<span class="at">useMultiCore=</span><span class="cn">FALSE</span>, <span class="at">numCores=</span><span class="cn">NULL</span>)</span>
<span id="cb8-5"><a href="#cb8-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb8-6"><a href="#cb8-6" aria-hidden="true" tabindex="-1"></a><span class="co"># Aggregating consensus clusters</span></span>
<span id="cb8-7"><a href="#cb8-7" aria-hidden="true" tabindex="-1"></a><span class="fu">consensusCluster</span>(myTSSr, <span class="at">dis =</span> <span class="dv">50</span>, <span class="at">useMultiCore =</span> <span class="cn">FALSE</span>)</span></code></pre></div>
<p>Core promoter shape</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Calculating core promoter shape score</span></span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="fu">shapeCluster</span>(myTSSr,<span class="at">clusters =</span> <span class="st">&quot;consensusClusters&quot;</span>, <span class="at">method =</span> <span class="st">&quot;PSS&quot;</span>,</span>
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a>             <span class="at">useMultiCore=</span> <span class="cn">FALSE</span>, <span class="at">numCores =</span> <span class="cn">NULL</span>)</span></code></pre></div>
<p>Annotation core promoters</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Assign clusters to the annotated features</span></span>
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="fu">annotateCluster</span>(myTSSr,<span class="at">clusters =</span> <span class="st">&quot;consensusClusters&quot;</span>,<span class="at">filterCluster =</span> <span class="cn">TRUE</span>,</span>
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a>              <span class="at">filterClusterThreshold =</span> <span class="fl">0.02</span>, <span class="at">annotationType =</span> <span class="st">&quot;genes&quot;</span></span>
<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a>              ,<span class="at">upstream=</span><span class="dv">1000</span>, <span class="at">upstreamOverlap =</span> <span class="dv">500</span>, <span class="at">downstream =</span> <span class="dv">0</span>)</span>
<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb10-6"><a href="#cb10-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Annotating...</span></span></code></pre></div>
<p>Differential expression analysis</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Assign clusters to the annotated features</span></span>
<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a><span class="fu">deGene</span>(myTSSr,<span class="at">comparePairs=</span><span class="fu">list</span>(<span class="fu">c</span>(<span class="st">&quot;control&quot;</span>,<span class="st">&quot;treat&quot;</span>)), </span>
<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a>       <span class="at">pval =</span> <span class="fl">0.01</span>,<span class="at">useMultiCore=</span><span class="cn">FALSE</span>, <span class="at">numCores=</span><span class="cn">NULL</span>)</span>
<span id="cb11-4"><a href="#cb11-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb11-5"><a href="#cb11-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Calculating gene differential expression...</span></span>
<span id="cb11-6"><a href="#cb11-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; converting counts to integer mode</span></span>
<span id="cb11-7"><a href="#cb11-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; estimating size factors</span></span>
<span id="cb11-8"><a href="#cb11-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; estimating dispersions</span></span>
<span id="cb11-9"><a href="#cb11-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; gene-wise dispersion estimates</span></span>
<span id="cb11-10"><a href="#cb11-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; mean-dispersion relationship</span></span>
<span id="cb11-11"><a href="#cb11-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; final dispersion estimates</span></span>
<span id="cb11-12"><a href="#cb11-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; fitting model and testing</span></span></code></pre></div>
<p>Core promoter shifts</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Calcuate core promoter shifts</span></span>
<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a><span class="fu">shiftPromoter</span>(myTSSr,<span class="at">comparePairs=</span><span class="fu">list</span>(<span class="fu">c</span>(<span class="st">&quot;control&quot;</span>,<span class="st">&quot;treat&quot;</span>)), <span class="at">pval =</span> <span class="fl">0.01</span>)</span>
<span id="cb12-3"><a href="#cb12-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb12-4"><a href="#cb12-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Calculating core promoter shifts...</span></span></code></pre></div>
<p>Session info</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span>
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; R version 4.1.1 (2021-08-10)</span></span>
<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Platform: x86_64-apple-darwin17.0 (64-bit)</span></span>
<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Running under: macOS Mojave 10.14.6</span></span>
<span id="cb13-5"><a href="#cb13-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb13-6"><a href="#cb13-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Matrix products: default</span></span>
<span id="cb13-7"><a href="#cb13-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib</span></span>
<span id="cb13-8"><a href="#cb13-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib</span></span>
<span id="cb13-9"><a href="#cb13-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb13-10"><a href="#cb13-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; locale:</span></span>
<span id="cb13-11"><a href="#cb13-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8</span></span>
<span id="cb13-12"><a href="#cb13-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb13-13"><a href="#cb13-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; attached base packages:</span></span>
<span id="cb13-14"><a href="#cb13-14" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
<span id="cb13-15"><a href="#cb13-15" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb13-16"><a href="#cb13-16" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; other attached packages:</span></span>
<span id="cb13-17"><a href="#cb13-17" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] TSSr_0.99.4</span></span>
<span id="cb13-18"><a href="#cb13-18" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb13-19"><a href="#cb13-19" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; loaded via a namespace (and not attached):</span></span>
<span id="cb13-20"><a href="#cb13-20" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   [1] backports_1.2.1                        </span></span>
<span id="cb13-21"><a href="#cb13-21" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   [2] Hmisc_4.5-0                            </span></span>
<span id="cb13-22"><a href="#cb13-22" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   [3] BiocFileCache_2.0.0                    </span></span>
<span id="cb13-23"><a href="#cb13-23" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   [4] lazyeval_0.2.2                         </span></span>
<span id="cb13-24"><a href="#cb13-24" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   [5] splines_4.1.1                          </span></span>
<span id="cb13-25"><a href="#cb13-25" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   [6] BiocParallel_1.26.2                    </span></span>
<span id="cb13-26"><a href="#cb13-26" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   [7] usethis_2.0.1                          </span></span>
<span id="cb13-27"><a href="#cb13-27" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   [8] GenomeInfoDb_1.28.4                    </span></span>
<span id="cb13-28"><a href="#cb13-28" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   [9] ggplot2_3.3.5                          </span></span>
<span id="cb13-29"><a href="#cb13-29" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [10] digest_0.6.28                          </span></span>
<span id="cb13-30"><a href="#cb13-30" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [11] ensembldb_2.16.4                       </span></span>
<span id="cb13-31"><a href="#cb13-31" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [12] htmltools_0.5.2                        </span></span>
<span id="cb13-32"><a href="#cb13-32" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [13] fansi_0.5.0                            </span></span>
<span id="cb13-33"><a href="#cb13-33" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [14] ggfortify_0.4.12                       </span></span>
<span id="cb13-34"><a href="#cb13-34" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [15] magrittr_2.0.1                         </span></span>
<span id="cb13-35"><a href="#cb13-35" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [16] checkmate_2.0.0                        </span></span>
<span id="cb13-36"><a href="#cb13-36" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [17] memoise_2.0.0                          </span></span>
<span id="cb13-37"><a href="#cb13-37" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [18] BSgenome_1.60.0                        </span></span>
<span id="cb13-38"><a href="#cb13-38" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [19] cluster_2.1.2                          </span></span>
<span id="cb13-39"><a href="#cb13-39" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [20] remotes_2.4.1                          </span></span>
<span id="cb13-40"><a href="#cb13-40" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [21] Biostrings_2.60.2                      </span></span>
<span id="cb13-41"><a href="#cb13-41" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [22] annotate_1.70.0                        </span></span>
<span id="cb13-42"><a href="#cb13-42" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [23] matrixStats_0.61.0                     </span></span>
<span id="cb13-43"><a href="#cb13-43" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [24] prettyunits_1.1.1                      </span></span>
<span id="cb13-44"><a href="#cb13-44" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [25] jpeg_0.1-9                             </span></span>
<span id="cb13-45"><a href="#cb13-45" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [26] colorspace_2.0-2                       </span></span>
<span id="cb13-46"><a href="#cb13-46" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [27] blob_1.2.2                             </span></span>
<span id="cb13-47"><a href="#cb13-47" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [28] rappdirs_0.3.3                         </span></span>
<span id="cb13-48"><a href="#cb13-48" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [29] xfun_0.26                              </span></span>
<span id="cb13-49"><a href="#cb13-49" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [30] dplyr_1.0.7                            </span></span>
<span id="cb13-50"><a href="#cb13-50" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [31] callr_3.7.0                            </span></span>
<span id="cb13-51"><a href="#cb13-51" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [32] crayon_1.4.1                           </span></span>
<span id="cb13-52"><a href="#cb13-52" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [33] RCurl_1.98-1.5                         </span></span>
<span id="cb13-53"><a href="#cb13-53" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [34] genefilter_1.74.0                      </span></span>
<span id="cb13-54"><a href="#cb13-54" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [35] survival_3.2-13                        </span></span>
<span id="cb13-55"><a href="#cb13-55" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [36] VariantAnnotation_1.38.0               </span></span>
<span id="cb13-56"><a href="#cb13-56" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [37] glue_1.4.2                             </span></span>
<span id="cb13-57"><a href="#cb13-57" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [38] gtable_0.3.0                           </span></span>
<span id="cb13-58"><a href="#cb13-58" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [39] zlibbioc_1.38.0                        </span></span>
<span id="cb13-59"><a href="#cb13-59" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [40] XVector_0.32.0                         </span></span>
<span id="cb13-60"><a href="#cb13-60" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [41] DelayedArray_0.18.0                    </span></span>
<span id="cb13-61"><a href="#cb13-61" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [42] pkgbuild_1.2.0                         </span></span>
<span id="cb13-62"><a href="#cb13-62" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [43] BiocGenerics_0.38.0                    </span></span>
<span id="cb13-63"><a href="#cb13-63" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [44] scales_1.1.1                           </span></span>
<span id="cb13-64"><a href="#cb13-64" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [45] BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0</span></span>
<span id="cb13-65"><a href="#cb13-65" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [46] DBI_1.1.1                              </span></span>
<span id="cb13-66"><a href="#cb13-66" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [47] Rcpp_1.0.7                             </span></span>
<span id="cb13-67"><a href="#cb13-67" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [48] xtable_1.8-4                           </span></span>
<span id="cb13-68"><a href="#cb13-68" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [49] progress_1.2.2                         </span></span>
<span id="cb13-69"><a href="#cb13-69" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [50] htmlTable_2.2.1                        </span></span>
<span id="cb13-70"><a href="#cb13-70" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [51] foreign_0.8-81                         </span></span>
<span id="cb13-71"><a href="#cb13-71" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [52] bit_4.0.4                              </span></span>
<span id="cb13-72"><a href="#cb13-72" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [53] Formula_1.2-4                          </span></span>
<span id="cb13-73"><a href="#cb13-73" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [54] stats4_4.1.1                           </span></span>
<span id="cb13-74"><a href="#cb13-74" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [55] htmlwidgets_1.5.4                      </span></span>
<span id="cb13-75"><a href="#cb13-75" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [56] httr_1.4.2                             </span></span>
<span id="cb13-76"><a href="#cb13-76" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [57] RColorBrewer_1.1-2                     </span></span>
<span id="cb13-77"><a href="#cb13-77" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [58] calibrate_1.7.7                        </span></span>
<span id="cb13-78"><a href="#cb13-78" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [59] ellipsis_0.3.2                         </span></span>
<span id="cb13-79"><a href="#cb13-79" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [60] pkgconfig_2.0.3                        </span></span>
<span id="cb13-80"><a href="#cb13-80" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [61] XML_3.99-0.8                           </span></span>
<span id="cb13-81"><a href="#cb13-81" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [62] Gviz_1.36.2                            </span></span>
<span id="cb13-82"><a href="#cb13-82" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [63] nnet_7.3-16                            </span></span>
<span id="cb13-83"><a href="#cb13-83" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [64] dbplyr_2.1.1                           </span></span>
<span id="cb13-84"><a href="#cb13-84" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [65] locfit_1.5-9.4                         </span></span>
<span id="cb13-85"><a href="#cb13-85" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [66] utf8_1.2.2                             </span></span>
<span id="cb13-86"><a href="#cb13-86" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [67] tidyselect_1.1.1                       </span></span>
<span id="cb13-87"><a href="#cb13-87" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [68] rlang_0.4.11                           </span></span>
<span id="cb13-88"><a href="#cb13-88" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [69] AnnotationDbi_1.54.1                   </span></span>
<span id="cb13-89"><a href="#cb13-89" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [70] munsell_0.5.0                          </span></span>
<span id="cb13-90"><a href="#cb13-90" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [71] tools_4.1.1                            </span></span>
<span id="cb13-91"><a href="#cb13-91" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [72] cachem_1.0.6                           </span></span>
<span id="cb13-92"><a href="#cb13-92" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [73] cli_3.0.1                              </span></span>
<span id="cb13-93"><a href="#cb13-93" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [74] generics_0.1.0                         </span></span>
<span id="cb13-94"><a href="#cb13-94" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [75] RSQLite_2.2.8                          </span></span>
<span id="cb13-95"><a href="#cb13-95" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [76] devtools_2.4.2                         </span></span>
<span id="cb13-96"><a href="#cb13-96" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [77] evaluate_0.14                          </span></span>
<span id="cb13-97"><a href="#cb13-97" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [78] stringr_1.4.0                          </span></span>
<span id="cb13-98"><a href="#cb13-98" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [79] fastmap_1.1.0                          </span></span>
<span id="cb13-99"><a href="#cb13-99" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [80] yaml_2.2.1                             </span></span>
<span id="cb13-100"><a href="#cb13-100" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [81] processx_3.5.2                         </span></span>
<span id="cb13-101"><a href="#cb13-101" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [82] knitr_1.36                             </span></span>
<span id="cb13-102"><a href="#cb13-102" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [83] bit64_4.0.5                            </span></span>
<span id="cb13-103"><a href="#cb13-103" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [84] fs_1.5.0                               </span></span>
<span id="cb13-104"><a href="#cb13-104" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [85] purrr_0.3.4                            </span></span>
<span id="cb13-105"><a href="#cb13-105" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [86] KEGGREST_1.32.0                        </span></span>
<span id="cb13-106"><a href="#cb13-106" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [87] AnnotationFilter_1.16.0                </span></span>
<span id="cb13-107"><a href="#cb13-107" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [88] xml2_1.3.2                             </span></span>
<span id="cb13-108"><a href="#cb13-108" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [89] biomaRt_2.48.3                         </span></span>
<span id="cb13-109"><a href="#cb13-109" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [90] compiler_4.1.1                         </span></span>
<span id="cb13-110"><a href="#cb13-110" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [91] rstudioapi_0.13                        </span></span>
<span id="cb13-111"><a href="#cb13-111" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [92] filelock_1.0.2                         </span></span>
<span id="cb13-112"><a href="#cb13-112" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [93] curl_4.3.2                             </span></span>
<span id="cb13-113"><a href="#cb13-113" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [94] png_0.1-7                              </span></span>
<span id="cb13-114"><a href="#cb13-114" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [95] testthat_3.0.4                         </span></span>
<span id="cb13-115"><a href="#cb13-115" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [96] tibble_3.1.4                           </span></span>
<span id="cb13-116"><a href="#cb13-116" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [97] geneplotter_1.70.0                     </span></span>
<span id="cb13-117"><a href="#cb13-117" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [98] stringi_1.7.4                          </span></span>
<span id="cb13-118"><a href="#cb13-118" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;  [99] ps_1.6.0                               </span></span>
<span id="cb13-119"><a href="#cb13-119" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [100] GenomicFeatures_1.44.2                 </span></span>
<span id="cb13-120"><a href="#cb13-120" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [101] desc_1.4.0                             </span></span>
<span id="cb13-121"><a href="#cb13-121" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [102] lattice_0.20-45                        </span></span>
<span id="cb13-122"><a href="#cb13-122" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [103] ProtGenerics_1.24.0                    </span></span>
<span id="cb13-123"><a href="#cb13-123" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [104] Matrix_1.3-4                           </span></span>
<span id="cb13-124"><a href="#cb13-124" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [105] vctrs_0.3.8                            </span></span>
<span id="cb13-125"><a href="#cb13-125" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [106] pillar_1.6.3                           </span></span>
<span id="cb13-126"><a href="#cb13-126" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [107] lifecycle_1.0.1                        </span></span>
<span id="cb13-127"><a href="#cb13-127" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [108] data.table_1.14.2                      </span></span>
<span id="cb13-128"><a href="#cb13-128" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [109] bitops_1.0-7                           </span></span>
<span id="cb13-129"><a href="#cb13-129" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [110] rtracklayer_1.52.1                     </span></span>
<span id="cb13-130"><a href="#cb13-130" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [111] GenomicRanges_1.44.0                   </span></span>
<span id="cb13-131"><a href="#cb13-131" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [112] R6_2.5.1                               </span></span>
<span id="cb13-132"><a href="#cb13-132" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [113] BiocIO_1.2.0                           </span></span>
<span id="cb13-133"><a href="#cb13-133" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [114] latticeExtra_0.6-29                    </span></span>
<span id="cb13-134"><a href="#cb13-134" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [115] gridExtra_2.3                          </span></span>
<span id="cb13-135"><a href="#cb13-135" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [116] IRanges_2.26.0                         </span></span>
<span id="cb13-136"><a href="#cb13-136" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [117] sessioninfo_1.1.1                      </span></span>
<span id="cb13-137"><a href="#cb13-137" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [118] dichromat_2.0-0                        </span></span>
<span id="cb13-138"><a href="#cb13-138" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [119] MASS_7.3-54                            </span></span>
<span id="cb13-139"><a href="#cb13-139" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [120] assertthat_0.2.1                       </span></span>
<span id="cb13-140"><a href="#cb13-140" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [121] pkgload_1.2.2                          </span></span>
<span id="cb13-141"><a href="#cb13-141" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [122] SummarizedExperiment_1.22.0            </span></span>
<span id="cb13-142"><a href="#cb13-142" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [123] DESeq2_1.32.0                          </span></span>
<span id="cb13-143"><a href="#cb13-143" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [124] rprojroot_2.0.2                        </span></span>
<span id="cb13-144"><a href="#cb13-144" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [125] rjson_0.2.20                           </span></span>
<span id="cb13-145"><a href="#cb13-145" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [126] withr_2.4.2                            </span></span>
<span id="cb13-146"><a href="#cb13-146" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [127] GenomicAlignments_1.28.0               </span></span>
<span id="cb13-147"><a href="#cb13-147" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [128] Rsamtools_2.8.0                        </span></span>
<span id="cb13-148"><a href="#cb13-148" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [129] S4Vectors_0.30.1                       </span></span>
<span id="cb13-149"><a href="#cb13-149" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [130] GenomeInfoDbData_1.2.6                 </span></span>
<span id="cb13-150"><a href="#cb13-150" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [131] parallel_4.1.1                         </span></span>
<span id="cb13-151"><a href="#cb13-151" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [132] hms_1.1.1                              </span></span>
<span id="cb13-152"><a href="#cb13-152" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [133] grid_4.1.1                             </span></span>
<span id="cb13-153"><a href="#cb13-153" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [134] rpart_4.1-15                           </span></span>
<span id="cb13-154"><a href="#cb13-154" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [135] tidyr_1.1.4                            </span></span>
<span id="cb13-155"><a href="#cb13-155" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [136] rmarkdown_2.11                         </span></span>
<span id="cb13-156"><a href="#cb13-156" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [137] MatrixGenerics_1.4.3                   </span></span>
<span id="cb13-157"><a href="#cb13-157" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [138] biovizBase_1.40.0                      </span></span>
<span id="cb13-158"><a href="#cb13-158" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [139] Biobase_2.52.0                         </span></span>
<span id="cb13-159"><a href="#cb13-159" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [140] base64enc_0.1-3                        </span></span>
<span id="cb13-160"><a href="#cb13-160" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [141] restfulr_0.0.13</span></span></code></pre></div>
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